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Are you using a tool to get this certificate? I wasn't aware of Microsoft Azure using Let's Encrypt for certificates automatically and most people use a tool if they want a Let's Encrypt certificates. Others just use Microsoft provided certificates (I don't know who the CA for that is).
For people that use Let's Encrypt certificates in azure they typically (to my knowledge) either:
populate a cert in KeyVault (using a tool to request the cert then push it to keyvault) then use that in their service
use a tool to get a certificate then apply it directly to the azure service (application gateway etc)
There are many possible tools to do that, it just depends what you used.